Research workbench
Cryptococcus neoformans protein farnesyltransferase in complex with fpp and L-778,123
Analyse Cryptococcus neoformans protein farnesyltransferase in complex with fpp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q7A
- Type
- protein
- Length
- 800 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyltransferase alpha subunit; Farnesyltransferase beta subunit
- Ligands
- 3FX, FPP, 778, GLC, FRU, ZN, SO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyltransferase alpha subunit | protein | 315 | 66% helix, 0% strand | — |
| B | Farnesyltransferase beta subunit | protein | 485 | 50% helix, 7% strand | — |
Ligands and binding sites
- 3FX · (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid · ligand · 3 copies · chains B, A
- FPP · Farnesyl diphosphate · ligand · chains A, B
- 778 · 4-[(5-{[4-(3-chlorophenyl)-3-oxopiperazin-1-yl]methyl}-1H-imidazol-1-yl)methyl]benzonitrile · ligand · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 3 copies · chains A, B
- ZN · Zinc ion · metal · chains B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.75 | 0.85 | 44 | GLC, FRU |
| 2 | 847 | 0.74 | 0.78 | 67 | SO4, FPP, 778 |
| 3 | 365 | 0.69 | 0.81 | 32 | empty |
| 4 | 506 | 0.64 | 0.77 | 45 | empty |
| 5 | 190 | 0.48 | 0.76 | 28 | GLC, FRU, 3FX |
Interfaces
1 interface between chains.
- A–B · 3836 Ų buried · 68 hydrogen bonds · protein-protein
Compared structures
- 3Q7A · Cryptococcus neoformans protein farnesyltransferase in complex with FPP and L-778,123 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3Q7A · PDBe 3Q7A
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